title: Microglia, F5-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F5-p1-421_Female_Dicer_KO_PS19

status: Public on Nov 05 2019

type: SRA

city: San Francisco

first: Lay

last: Kodama

state: CA

address: 1650 Owens St.

department: Gladstone Institute of Neurological Disease

country: USA

institute: University of California San Francisco

description: mRNA expression in microglia

library_source: transcriptomic

data_processing:
Prinseq (version 0.20.4) was first used to filter sequencing reads shorter than 30 bp (-min_len 30), trim the first 10 bp at the 5’-end (-trim_left 10) of the reads, trim reads with low quality from the 3’-end (-trim_qual_right 25) and remove low complexity reads (-lc_method entropy, -lc_threshold 65).
Trim Galore (version 0.4.3) was applied to trim the Nextera adapters (--stringency 1).
The remaining reads were aligned to the mm10 genome by calling STAR (version 2.5.3a) with the following options: --outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outSAMstrandField intronMotif.
Picard was then used to remove the duplicate reads (VALIDATION_STRINGENCY=LENIENT, REMOVE_DUPLICATES=true).
The aligned reads were converted to counts for each gene by using HTSeq (-m intersection-nonempty, -s no)
Genome_build: mm10
Supplementary_files_format_and_content: Common delimited file (tsv) containing 721 samples and mapped gene counts.

molecule: total RNA

organism: Mus musculus

source_name: FACS isolated adult microglia

extract_protocol:
In online methods
Smart-Seq2 protocol (in online methods)

tag: strain

tag: tissue

value: brain

tag: age

value: 9 months

tag: Sex

value: Female

tag: gate


title: Microglia, F4-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia

value: Male


title: Microglia, F4-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F3-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F4-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F3-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F4-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F4-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F4-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F3-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F3-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F4-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F2-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F3-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F2-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F3-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F3-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F2-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F4-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F2-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F2-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F2-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F2-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F5-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F5-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F2-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F12-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F12-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F12-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F12-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F12-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F11-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F11-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F11-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F10-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F11-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F11-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F1-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F10-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F10-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F1-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F10-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F10-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F10-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F1-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F1-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F1-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F11-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F10-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F1-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E9-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E9-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F12-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E9-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E9-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E9-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F12-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F10-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E9-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F1-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E9-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E8-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E9-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E8-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E7-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E7-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E8-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E8-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E7-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E8-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E7-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E8-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E7-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E7-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E8-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E7-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E6-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E6-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E8-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E6-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E6-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E6-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E6-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E6-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E5-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E5-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E6-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E5-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E5-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E5-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E5-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E4-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E4-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E3-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E3-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E3-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E3-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E4-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E4-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E4-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E3-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E4-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E3-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E2-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E3-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E3-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E2-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E2-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E2-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E12-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E2-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E2-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E2-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E2-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E12-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E4-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E12-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E5-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E12-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E4-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E11-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E12-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E11-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E10-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E10-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E10-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E10-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E12-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E11-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E10-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E10-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E10-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E12-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E1-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E12-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E11-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E11-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E1-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E11-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E1-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E1-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E10-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E1-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E1-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D9-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E1-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D9-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D9-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D9-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D9-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D9-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D9-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D8-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D8-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, E1-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D8-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D7-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D8-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D8-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D8-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D8-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D8-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D6-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D6-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D7-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D6-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D7-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D7-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D7-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D7-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D9-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D6-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D6-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D6-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D6-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D5-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D4-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D5-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D4-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D6-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D5-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D5-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D5-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D4-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D5-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D5-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D7-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D5-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D7-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D4-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D4-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D3-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D3-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D3-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D3-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D3-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D4-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D3-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D4-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D2-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D2-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D3-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D4-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D2-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D2-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D2-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D12-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D2-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D2-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D2-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D12-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D12-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D12-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D11-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D12-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D12-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D12-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D3-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D11-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D12-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D11-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D11-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D11-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D11-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D11-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D10-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D11-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D10-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D10-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D10-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D10-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D10-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D1-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D1-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D1-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D1-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D1-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D1-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D10-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C9-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D1-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C8-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C9-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C9-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C8-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C9-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C8-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C8-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C9-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D1-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, D10-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C8-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C9-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C8-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C9-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C8-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C8-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C9-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C7-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C7-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C7-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C6-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C6-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C7-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C7-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C6-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C6-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C5-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C6-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C6-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C5-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C7-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C5-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C5-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C4-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C5-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C4-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C4-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C5-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C4-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C5-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C4-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C4-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C3-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C7-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C7-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C6-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C6-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C3-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C5-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C3-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C3-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C3-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C3-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C2-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C3-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C4-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C2-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C12-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C2-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C12-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C12-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C12-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C2-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C2-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C2-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C12-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C12-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C11-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C11-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C11-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C11-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C4-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C3-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C11-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C11-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C10-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C10-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C2-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C12-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C10-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C11-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C10-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C10-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C1-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C1-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C1-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C1-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C12-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C10-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C1-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B9-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C1-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B9-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C1-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B9-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B9-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B9-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B9-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B9-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B9-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B8-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B8-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C10-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, C10-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B8-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B8-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B8-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B7-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B8-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B8-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B6-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B7-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B7-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B7-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B6-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B6-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B8-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B6-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B6-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B6-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B5-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B7-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B7-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B5-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B5-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B5-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B5-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B4-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B7-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B5-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B4-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B5-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B4-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B4-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B6-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B4-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B4-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B4-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B6-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B7-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B3-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B3-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B2-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B2-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B3-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B3-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B3-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B3-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B3-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B2-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B2-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B2-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B2-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B2-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B2-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B12-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B12-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B12-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B12-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B12-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B12-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B12-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B11-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B12-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B10-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B11-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B11-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B10-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B10-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B10-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B11-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B11-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B10-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B1-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B11-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B10-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B10-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B1-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B1-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A9-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B1-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A9-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A9-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B1-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A9-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A9-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A9-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A8-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A8-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A8-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A8-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A8-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A8-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B1-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A6-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A6-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A7-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A7-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A7-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A8-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A6-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B10-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A7-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A8-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A7-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A5-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, B1-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A6-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A6-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A5-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A5-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A4-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A6-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A5-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A4-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A6-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A4-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A4-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A5-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A7-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A3-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A4-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A3-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A3-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A4-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A4-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A2-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A7-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A5-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A3-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A3-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A3-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A5-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A3-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A2-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A3-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A12-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A12-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A2-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A2-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A2-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A12-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A2-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A12-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A12-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A12-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A11-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A11-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A11-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A11-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A11-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A12-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A12-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A2-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A11-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A10-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A10-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A2-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A10-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A10-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A1-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A10-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A10-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A1-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A1-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A1-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A1-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A11-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A1-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Young_Female_Dicer_PS_1

address: 1650 Owens St

department: J David Gladstone Institutes

institute: University of California, San Francisco

description:
mRNA expression in microglia
RNA_seq_all_counts_new

data_processing:
RNA-seq reads were mapped with the Bluebee Genomics Platform and using the GENCODE  mouse genome GRCm38
Counts   were normalized with the trimmed mean normalization method
Genome_build: GRCm38 for mRNA-seq
Supplementary_files_format_and_content: Raw read counts in csv format

source_name: Freshly isolated adult microglia

extract_protocol:
RNeasy mini kit (Qiagen, 74104) was used for RNA isolation and Oligo(dT) beads were used to enrich for mRNA
cDNA library generation was done  using the QuantSeq 3´ mRNA-Seq Library Prep Kit for Illumina (Lexogen)

tag: cell type

value: Freshly isolated adult microglia

value: 3 months


title: Young_Female_Dicer_PS_2


title: Young_Male_Dicer_PS_2


title: Young_Male_Dicer_PS_4


title: Young_Male_Dicer_PS_3


title: Young_Male_Dicer_PS_1


title: Female_PS_4


title: Female_PS_1


title: Female_PS_2


title: Male_PS_3


title: Male_PS_1


title: Microglia, A1-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, A1-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Female_Dicer_PS_2


title: Extracted RNA from hepatocyte organoids grown in BME, passage 18, replicate 1

city: Würzburg

first: Kai

last: Kretzschmar

address: Josef-Schneider-Str. 2

country: Germany

institute: University Hospital Würzburg

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the human genome release hg19 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
Genome_build: hg19
Supplementary_files_format_and_content: coutb files contain UMI barcode normalised abundance counts

organism: Homo sapiens

source_name: Liver

extract_protocol:
For bulk sequencing, mRNA was isolated from culutred organoids by Trizol method according to manufacter's protocol. RNA-sequencing libraries were prepared based on the DESeq2 method (Hashimshony et al., 2016; Love et al., 2014) with modifications (Kretzschmar et al., 2019)
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

value: hepatocyte organoids

tag: growth

value: grown in BME


title: Extracted RNA from hepatocyte organoids grown in BME, passage 30, replicate 1


title: Female_Dicer_PS_4


title: Male_Dicer_PS_4


title: Female_Dicer_PS_1


title: Extracted RNA from hepatocyte organoids grown in BME, passage 29, replicate 2


title: Female_Dicer_PS_3


title: Extracted RNA from hepatocyte organoids grown in BME, passage 29, replicate 1


title: Extracted RNA from hepatocyte organoids grown in BME, passage 30, replicate 2


title: Extracted RNA from hepatocyte organoids grown in BME, passage 18, replicate 2


title: Extracted RNA from hepatocyte organoids grown in ECM, passage 18, replicate 2

value: grown in ECM


title: Male_Dicer_PS_2


title: Male_Dicer_PS_1


title: Extracted RNA from hepatocyte organoids grown in ECM, passage 18, replicate 1


title: Male_PS_2


title: Extracted RNA from hepatocyte organoids grown in ECM, passage 30, replicate 2


title: Extracted RNA from hepatocyte organoids grown in ECM, passage 30, replicate 1


title: Male_Dicer_PS_3


title: Extracted RNA from hepatocyte organoids grown in ECM, passage 29, replicate 2


title: Extracted RNA from hepatocyte organoids grown in ECM, passage 29, replicate 1


title: ♂PWK x ♀C57 4cell rep2

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

country: China

institute: Beijing Institute of Radiation Medicine

data_processing:
Sequence are mapped to C57 refernece and PWK reference seperately
The alignments with PWK reference are converted to C57 coordinate.
The converted alignment and the original C57-based alignment are combined into one alignment and splited into three files based on the reads' origins
C57-origin and PWK-origin reads counts are calculated using Htseq count for each genes seperately
Allelic ratio of genes is calculated based on the read counts.
Genome_build: mm10
Supplementary_files_format_and_content: plain txt file, each contains two column. First column means the gene ID, the second column means the allelic ratio

source_name: ♂PWK x ♀C57 4cell cells

growth_protocol: Embryos in this study were derived from interbreeding of two mouse strains, C57BL/6J and PWK/PhJ. 4 to 8 week-old C57BL/6J female mice were mated with adult PWK/PhJ males, while 4 to 8 week-old PWK/PhJ female mice were mated with adult C57BL/6J males.

extract_protocol:
Female mice were superovulated by 5 IU PMSG injection, followed by 5 IU hCG injection 48 h later. Embryos at different stages were collected after hCG injection at different time periods.
The collected embryos were washed twice with 1xPBS and were lysed in RLT lysis buffer (Qiagen) containing 40 mM DTT. Subsequently, the total RNA was extracted using RNeasy Micro kit (Qiagen) according to the manufacturer’s recommendations. Then the poly (A) mRNA was isolated with NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB), followed by first strand cDNA synthesis using random primers by ProtoScript II Reverse Transcriptase. Double-strand cDNA was synthesized with second strand synthesis buffer and enzyme mix. The purified cDNA was used for library construction with NEBNext ultra RNA library prep kit for Illimina. The quality and quantity of the libraries was assessed and defined by Fragment Analyzer (AATI) and Qubit dsDNA HS Assay Kit, respectively.
The library sequencing was performed on Illumina HiSeq 4000 sequencers with paired-end 150-bp sequencing.

tag: female strain

tag: male strain

value: PWK/PhJ

tag: development stage

value: 4 cell


title: Extracted RNA from ductal organoids grown in BME, replicate 4

value: liver ductal organoids


title: ♂PWK x ♀C57 4cell rep1


title: ♂PWK x ♀C57 2cell mid rep2

source_name: ♂PWK x ♀C57 2cell mid cells

value: 2 cell mid


title: Extracted RNA from ductal organoids grown in BME, replicate 3


title: ♂PWK x ♀C57 2cell late rep2

source_name: ♂PWK x ♀C57 2cell late cells

value: 2 cell late


title: Extracted RNA from ductal organoids grown in BME, replicate 2


title: Extracted RNA from ductal organoids grown in BME, replicate 1


title: Extracted RNA from ductal organoids grown in ECM, replicate 3


title: Extracted RNA from ductal organoids grown in ECM, replicate 4


title: ♂PWK x ♀C57 2cell early rep2

source_name: ♂PWK x ♀C57 2cell early cells

value: 2 cell early


title: ♂PWK x ♀C57 zygote rep2

source_name: ♂PWK x ♀C57 zygote cells

value: zygote


title: Extracted RNA from ductal organoids grown in ECM, replicate 2


title: Extracted RNA from ductal organoids grown in ECM, replicate 1


title: ♂C57 x ♀PWK 4cell rep2

source_name: ♂C57 x ♀PWK 4cell cells


title: ♂C57 x ♀PWK 4cell rep1


title: ♂PWK x ♀C57 2cell early rep1


title: MINCE_EdU_Chase_2

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

country: France

institute: Institut Pasteur

library_source: genomic

data_processing:
Library strategy: MINCE-seq
ChIP-seq: Reads aligned with Bowtie2 with options “-k 10”. Reads were filtered for mapping quality 255 and edit distance <= 4. Reads with identical barcode, alignment position & strand  were treated as PCR-duplicates and collapsed. Peaks called with MACS2 with options “callpeak -q 0.2 -g mm”. BigWig files were generated by extending reads to mean fragment length.
Mnase-seq & MINCE-seq: Paired end reads were trimmed by alignment for reverse complementary regions surrounded by relevant adapters. Reads were aligned using Bowtie2 with options “-k 10 -I 0 -X 1000 --no-discordant --no-mixed”. Pairs were filtered for mapping quality 255 and mean edit-distance <= 4. BigWig files were generated by marking the +/-20bp of the midpoint of fragments in [140, 200]bp.
Genome_build: mm10
Supplementary_files_format_and_content: BigWigFiles

molecule: genomic DNA

source_name: embryonic stem cell

growth_protocol: ES cells (wild-type E14Tg2a and CTCF-aid derivatives) were cultured on 0.1% gelatine (SIGMA, G1890-100G) in DMEM+GlutaMax-I (Gibco, 31966-021), 10% FCS (Gibco 10270- 098), 100μM β-mercaptoethanol (Gibco, 31350-010), 1×MEM non-essential amino acids (Gibco, 1140-035) and 10ng/ml recombinant LIF (MILTENYI BIOTEC, 130-099-895). ES cells were passaged 1:10 every 2–3 days. NIH3T3 and C2C12 cells were cultured in DMEM + GlutaMax-I supplemented with 10% FCS. NIH3T3 and C2C12 were passaged 1:15 and 1/20, respectively, every 3 days.

extract_protocol: MINCE-seq: 1) Chromatin Preparation after trypsinisation, 120 × 106 cells per sample were fixed with 1% formaldehyde (Thermo, 28908; 10 min at room temperature with occasional mixing) and quenched with 0.125M Glycine (5 min). Fixed cells, after being washed twice with PBS,  were lysed for 10 min on a rotating wheel at 4oC in 5 mL of lysis buffer (50mM HEPES pH 7.8/ 150mM NaCl/ 0.5% v/v IGEPAL/ 0.25% v/v Triton-X/ 10% v/v Glycerol) supplemented with 1× protease inhibitor cocktail (PIC-Roche, 04 693 116 001). After centrifugation, the cells were resuspended in 4 ml Wash Buffer (WB: 10mM Tris-HCl pH 8/ 200mM NaCl)  supplemented with 0.5mM DTT and incubated for 10 min on a rotating wheel at 4o C. Nuclei were pelleted for 5 min at 3000 rpm at 4°C  and resuspended in 1.5 ml RIPA buffer (10mM Tris-HCl pH 8/ 140mM NaCl/ 1% Triton-X/ 0.1% Sodium-Deoxycholate/ 0.1% SDS) freshly supplemented with 1× protease inhibitor cocktail  and 1mM CaCl2.  2) MNase Digestion Samples were equally split in 3 (1.5 ml tubes) and incubated for 10 min in a water bath at 37oC. MNase (Thermo Scientific EN0181) was diluted at 80U/μl in RIPA buffer freshly supplemented with 1× protease inhibitor cocktail and 1mM CaCl2. The digestion was carried out by adding MNase at a final concentration of 6U per million cells and incubation for 5 min at 37oC with occasional mixing. Digestions were stopped by placing tubes on ice and by adding 2× STOP Buffer (2% Triton/ 0.2% SDS/ 300mM NaCl/ 10mM EDTA). Digested chromatin was recovered by overnight rotation at 4oC followed by centrifugation at 4°C  at maximum speed for 10 min. 3) DNA Extraction The chromatin was equally distributed in 1.5 ml tubes and the crosslinking reverted overnight at 65°C in the presence of 1% SDS and shaking (800 rpm). The next day the samples were incubated for 2h at 56°C with 5 μl Proteinase K (GEXPRK01B5 Eurobio) and processed through phenol/chlorophorm extraction and ethanol precipitation. DNA was resuspended in a total volume of 0.4 ml Ultra Pure Nuclease free water. RNase digestion was carried out with 5 μl RNase A (EN0531 Thermo Scientific) for 2 hours at 37°C . The DNA was purified and precipitated again and resuspended in 51 μl Ultra Pure Nuclease free water. 1 μl of DNA was further diluted and the fragment sizes were analysed with a D1000 HS Screentape (Agilent 5067-5584) on an Agilent Tapestation. 4) CLICK-reaction streptavidin pull-down each DNA sample (50 μl) was supplemented, in order, with the following buffers: 342.5 μl of 100 mM Potassium Phosphate Buffer (15433339 Fisher Scientific); 50 μl of 10 mM Biotin-TEG Azide (762024 Sigma ) resuspended in DMSO; 7.5 μl of pre-mixed Cupric Sulfate Pentahydrate (2.5 μl at 20mM; C8027 Sigma) and THTPA (5 μl at 50 mM; 762342 Sigma); 25 μl of 100 mM Aminoguanidine Hydrochloride (396494 Sigma); 25 μl of 100 mM Sodium Ascorbate (A4034 Sigma). After briefly vortexing, the reactions were performed for 1.5 hours at room temperature protected from light, and  DNA was subsequently ethanol-precipitated and resuspended in 400 μl ultra pure water. Twenty microliters were kept as input and the rest (380 μl) were used for streptavidin pull down. For this, 25 μl M-280 streptavidin magnetic beads (10292593 Thermo Scientific) per reaction were washed 3 times (10 min rotation at room temperature per wash) with 1 ml 1× Wash and Binding buffer (W&B; 2×:  10 mM Tris-HCl pH 7.5; 1 mM EDTA; 2 M NaCl; 0.2% Tween 20) and resuspended in 25 μl 1× W&B buffer. EdU-labelled DNA was then pulled down with 380 μl 2× W&B buffer and 25 μl washed beads (1 hour at room temperature on a rotating wheel). Beads were separated by placing the tubes on a magnetic rack and the unbound fraction was stored at -20oC. The beads were washed 3 times with 1ml W&B buffer (10 min at room temperature on a rotating wheel). Washed beads were resuspended in 100 μl TE/1% SDS and DNA was eluted with 20 μl Proteinase K (1 hour at 65oC with occasional vortexing). After adding TE to a final volume of 200 μl, the DNA was phenol/chloroform-extracted, ethanol-precipitated and resuspended in 20 μl ultra pure water.

treatment_protocol: To obtain early replicating cells, 15x106 live cells were seeded per 150 mm dish 24 hours prior to the beginning of each experiment (3 dishes per condition). The cells were incubated with pre-warmed medium containing 5 μM EdU for 2.5 min at 37oC. Next, the cells were either harvested and fixed (pulse) or, in parallel, washed with pre-warmed medium and incubated for 1h in the presence of 100 μM Thymidine for 1 hour at 37oC (chase).

value: embryonic stem cell

tag: cell subtype

tag: cell cycle

value: R

tag: treatment


title: ♂C57 x ♀PWK zygote rep2

source_name: ♂C57 x ♀PWK zygote cells


title: MINCE_EdU_Pulse_2


title: ♂C57 x ♀PWK zygote rep1


title: MINCE_Input_Chase_2


title: ♂C57 x ♀PWK 2cell late rep2

source_name: ♂C57 x ♀PWK 2cell late cells


title: ♂C57 x ♀PWK 2cell mid rep1

source_name: ♂C57 x ♀PWK 2cell mid cells


title: ♂PWK x ♀C57 2cell mid rep1


title: NIH3T3_INPUT_I_PFA_1

data_processing:
ChIP-seq: Reads aligned with Bowtie2 with options “-k 10”. Reads were filtered for mapping quality 255 and edit distance <= 4. Reads with identical barcode, alignment position & strand  were treated as PCR-duplicates and collapsed. Peaks called with MACS2 with options “callpeak -q 0.2 -g mm”. BigWig files were generated by extending reads to mean fragment length.
Mnase-seq & MINCE-seq: Paired end reads were trimmed by alignment for reverse complementary regions surrounded by relevant adapters. Reads were aligned using Bowtie2 with options “-k 10 -I 0 -X 1000 --no-discordant --no-mixed”. Pairs were filtered for mapping quality 255 and mean edit-distance <= 4. BigWig files were generated by marking the +/-20bp of the midpoint of fragments in [140, 200]bp.
Genome_build: mm10
Supplementary_files_format_and_content: BigWigFiles

source_name: fibroblasts

extract_protocol: ChIP-seq/Mnase-seq: For interphase, 2.5x106 fixed cells (1% formaldehyde for 10min followed by 5min with 0.125 M Glycine) were resuspended in 2ml swelling buffer (25mM Hepes pH 7.95, 10mM KCl, 10mM EDTA; freshly supplemented with 1× protease inhibitor cocktail – 04 693 116 001 PIC-Roche, and 0.5% IGEPAL), incubated for 30min on ice, and passed 40 times in a dounce homogenizer to recover nuclei. For mitotic cells, the homogenization step was omitted. Mitotic and interphase cells were then treated in parallel to sonicate the chromatin in 300μl of TSE150 (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl pH8, 150mM NaCl; freshly supplemented with 1× PIC) using 1.5ml tubes (Diagenode) and a Bioruptor Pico (Diagenode; 7 cycles divided into 30 s ON–30 s OFF sub-cycles at maximum power, in circulating ice-cold water). After centrifugation (30min, full speed, 4 °C), the supernatant was pre-cleared for 2h with 50μl of protein G Sepharose beads (P3296-5 ML Sigma) 50% slurry, previously blocked with BSA (500 μg/ml; 5931665103 Roche) and yeast tRNA (1 μg/ml; AM7119 Invitrogen). 20μl were set apart (input) before over-night immunoprecipitation at 4°C on a rotating wheel with 4µl of anti-CTCF (Active Motif 61311) or 4µl of anti-SMC1 (Bethyl Laboratories A300-055A) antibodies in 500μl of TSE150. Protein G beads (25μL 50% slurry) were added for 4 h rotating on-wheel at 4 °C. Beads were pelleted and washed for 15min rotating on-wheel at 4 °C with 1ml of the following buffers: 3 washes with TSE150, 1 wash with TSE500 (as TSE150 but 500 mM NaCl), 1 wash with Washing buffer (10mM Tris-HCl pH8, 0.25M LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 1mM EDTA), and 2 washes with TE (10mM Tris-HCl pH8, 1mM EDTA). Elution was performed in 100μl of elution buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl pH 8) for 15min at 65 °C after vigorous vortexing. Eluates were collected after centrifugation and beads rinsed in 150μl of TE-SDS1%. After centrifugation, the supernatant was pooled with the corresponding first eluate. For both immunoprecipitated and input chromatin, the crosslinking was reversed overnight at 65 °C, followed by proteinase K treatment, phenol/chloroform extraction and ethanol precipitation. H3 ChIP-seq was performed on MNase-digested chromatin using 2.5x106 cells fixed with formaldehyde as described above. Fixed cells were resuspended in 500µl of MNase buffer (50 mM Tris-HCl pH8, 1 mM CaCl2, 0.2% Triton X-100) supplemented with protease inhibitor cocktail (PIC; 04 693 116 001 Roche). Cells were pre-incubated for 10min at 37°C with 16U of MNase (Expressed in KUntiz, 1 Kunitz is equivalent to 10 gel units, NEB M0247S) added to the reaction. Cells were incubated for further 10min at 37°C, inverting the tubes occasionally. The reaction was stopped on ice by adding 500μl of 2×STOP buffer (2% Triton X-100, 0.2% SDS, 300mM NaCl, 10mM EDTA). Tubes were left rotating overnight on a wheel to allow diffusion of the digested fragments. The cell suspension was spun down and the supernatant stored at -80°C. Subsequently, 50µl of chromatin were brought to a final volume of 500µl with TSE150 (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl pH8, 150mM NaCl), freshly supplemented with protease inhibitor cocktail (PIC-Roche, 04 693 116 001), and ChIP was performed as described above using 5µg of anti-Histone H3 rabbit polyclonal (Abcam; ab1791).

treatment_protocol: To obtain mitotic ES cells (>95% purity as assessed by DAPI staining and microscopy), we used a nocodazole shake-off approach. To deplete CTCF-aid in interphase, cells were treated with 0.5mM auxin (IAA Sigma, I5148) for 2h; to deplete CTCF-aid in mitosis, the cells were first treated with nocodazole for 4h and then with nocodazole and IAA for 2h, after which they were harvested by shake-off. C2C12 cells were synchronised like ES cells except that slightly longer nocodazole treatment (7h) was required to improve the yield. NIH3T3 cells were first synchronised with a double thymidine block, followed by release and nocodazole treatment; first, 1.5x106 cells were seeded in 150mm dishes and grown with 2mM thymidine for 18h to enrich in cells arrested at the G1/S transition. After two washes with PBS, they were released for 8h in regular medium before being arrested again for 17h with 2mM Thymidine. After the double thymidine block the cells were washed twice with PBS and released in regular medium for 7h. Finally, cells were incubated with nocodazole for 6h and mitotic cells isolated by gentle tapping of the dishes against an immobilised surface.

value: fibroblasts

tag: chip antibody

value: INPUT

value: I


title: MINCE_Input_Pulse_2


title: ♂C57 x ♀PWK 2cell early rep2

source_name: ♂C57 x ♀PWK 2cell early cells


title: ♂PWK x ♀C57 2cell late rep1


title: ♂C57 x ♀PWK 2cell late rep1


title: NIH3T3_INPUT_M_PFA_1

value: M


title: C2C12_INPUT_M_PFA_1

source_name: myoblast cell line

value: myoblast cell line


title: C2C12_INPUT_I_PFA_1


title: CTCFAID_INPUT_M_minusIAA_PFA_1

value: CTCFAID

value: minusIAA


title: Female_Dicer_2

data_processing:
reads were mapped to mature miRNA from  mirBase with Bowtie2 for miRNA-seq and RNA-seq reads were mapped with the Bluebee Genomics Platform and using the GENCODE  mouse genome GRCm38
Batch effects were removed with the R package RUVSeq and normalized to in silico control genes for miRNA-seq
Counts  were normalized with the trimmed mean normalization method
Genome_build: mirBase for miRNA-seq, GRCm38 for mRNA-seq
Supplementary_files_format_and_content: Raw read counts in csv format

value: Freshly isolated adult microglia

value: 9 months

value: Female


title: Female_Dicer_1


title: ♂C57 x ♀PWK 2cell mid rep2

value: PWK/PhJ


title: Female_WT_1


title: Male_Dicer_4

value: Male


title: ♂PWK x ♀C57 zygote rep1


title: TG2A_INPUT_M_PFA_2


title: TG2A_INPUT_M_PFA_3


title: TG2A_INPUT_I_PFA_3


title: TG2A_INPUT_I_PFA_2


title: Male_Dicer_2


title: Male_Dicer_3


title: Male_Dicer_1


title: CTCFAID_CTCF_M_plusIAA_PFA_1

value: CTCF (Active Motif 61311)

value: plusIAA


title: CTCFAID_CTCF_M_plusIAA_PFA_2


title: Male_WT_5


title: ♂C57 x ♀PWK 2cell early rep1

value: 2 cell early


title: CTCFAID_CTCF_M_minusIAA_PFA_2

value: embryonic stem cell


title: Male_WT_3


title: CTCFAID_CTCF_M_minusIAA_PFA_1


title: Male_WT_2


title: CTCFAID_INPUT_I_minusIAA_PFA_1


title: Female_WT_3


title: Male_WT_4


title: Female_WT_2


title: Male_WT_1


title: CTCFAID_CTCF_I_plusIAA_PFA_2


title: GAR1414

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

institute: Helmholtz Zentrum München

data_processing:
STAR aligner was used for split-read alignment against the mouse genome assembly mm10 and UCSC known Gene annotation. To quantify the number of reads mapping to annotated genes we used HTseq-count
Genome_build: mm10
Supplementary_files_format_and_content: tsv files contain raw read count; they have two columns where the first column specifies the gene name and the second the actual read count

source_name: brown fat (BAT)

extract_protocol:
Total RNA was extracted from inguinal WAT, BAT, liver and muscle using Qiazol according to the manufacturer’s instructions (Qiazol Lysis Reagent, QIAGEN). The quality of the RNA was determined with the Agilent 2100 BioAnalyzer (RNA 6000 Nano Kit, Agilent). All samples had a RNA integrity number (RIN) value greater than .8
For library preparation, 1 µg of total RNA per sample was used. RNA molecules were poly(A) selected, fragmented, and reverse transcribed with the Elute, Prime, Fragment Mix (EPF, Illumina). End repair, A-tailing, adaptor ligation, and library enrichment were performed as described in the TruSeq Stranded mRNA Sample Preparation Guide (Illumina). RNA libraries were assessed for quality and quantity with the Agilent 2100 BioAnalyzer and the Quant-iT PicoGreen dsDNA Assay Kit (Life Technologies).
Strand-specific RNA libraries were sequenced as 100 bp paired-end runs on an Illumina HiSeq4000 platform.

value: brown fat (BAT)

tag: genotype

value: FGF21 KO

tag: gender

value: male


title: CTCFAID_CTCF_I_plusIAA_PFA_1

value: I


title: TG2A_SMC1_I_PFA_2

value: SMC1 (Bethyl Laboratories A300-055A)


title: GAR1413


title: NIH3T3_CTCF_M_PFA_1

value: fibroblasts

value: M


title: GAR1408

value: UCP1/FGF12 double KO


title: C2C12_CTCF_I_PFA_1

value: myoblast cell line


title: GAR1411


title: C2C12_CTCF_M_PFA_1


title: GAR1409


title: GAR1407


title: GAR1406


title: TG2A_CTCF_I_PFA_3


title: CTCFAID_CTCF_I_minusIAA_PFA_2

value: CTCFAID

value: minusIAA


title: GAR1404

value: UCP1 KO


title: CTCFAID_CTCF_I_minusIAA_PFA_1


title: GAR1403


title: GAR1412


title: NIH3T3_CTCF_I_PFA_1


title: Female_PS_3

value: Freshly isolated adult microglia

value: 9 months

value: Female


title: GAR1405


title: GAR1402


title: GAR1401


title: GAR1400


title: GAR1398

value: WT


title: GAR1434

source_name: inguinal white fat (iWAT)

value: inguinal white fat (iWAT)


title: GAR1396

value: brown fat (BAT)


title: GAR1397


title: GAR1433

value: FGF21 KO


title: GAR1432

value: male


title: GAR1399


title: GAR1395


title: GAR1430


title: GAR1429


title: GAR1431


title: C1_F3 (IM study)

type: RNA

city: Ljubljana

first: Spela

last: Baebler

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

description: pool of 2 individuals

hyb_protocol: Hybridizations and washes were performed using Gene Expression Hybridization Kit (Agilent Technologies) following manufactures protocol

scan_protocol: Hybridized slides were scanned on Agilent DNA Microarray Scanner and signals were extracted and quality control was performed using Feature Extraction 10.7.3.1 Software (Agilent Technologies).

data_processing: Microarray data analysis was performed in R environment (version 2.15.1) using Bioconductor’s libraries limma and vsn.

organism: Danio rerio

source_name: 4 months old zebrafish liver

label_protocol: Labelling, hybridization and scanning were performed by the IMGM (Germany). The total RNA was labelled with Cy-3 using Low Input Quick-Amp Labeling Kit One-Color (Agilent technologies) following manufacturers protocol

growth_protocol: The wild time (AB line) of zebrafish (Danio rerio) originated and was cultured at the Department of Aquaculture of Szent István University (Hungary). Prior to the study, the parent generation was maintained in a recirculation system that allowed continuous flow of water (ZebTec; Tecniplast Inc.) under a light regime of 14 h light/ 10 h dark. The parameters of the recirculation system water were as follows: temperature, 25 ±0.5 °C; pH, 7.4 ±0.2; and conductivity, 525 ±50 µS. During the study period, the zebrafish were maintained at 24 °C to 26 °C under a light regime of 14 h light/ 10 h dark. Fish were fed twice a day with SDS Small Gran granulated feed and twice a week, with Artemia. The animal protocol was approved by the Hungarian Animal Welfare Law .

extract_protocol: The RNA was isolated by Direct-zol RNA Miniprep (ZymoResearch) from liver of 6 individuals liver per exposure point from each of the two replicates. After RNA quality and quantity evaluation (Agilent Bioanalyzer, RNA 6000 Nano Kit, Eukaryote Assay), RNA from 1-3 individuals from same treatment, replicate and gender was pooled, DNase treated (Invitrogen DNaseI; 0.2 U/µg RNA) in 45 μl reactions and subsequently purified using RNeasy Mini Elute kit (Qiagen). Purified RNA was checked for integrity and quantity by Bioanalyzer.

treatment_protocol: Imatinib mesylate (sc-202180A, Santa Cruz Biotechnology) was diluted in the clean recirculation system water to final concentrations of the exposure of 0.01 µg/L (C1) and 1.0 µg/L (C2).  The control group was grown in the recirculation system water alone. All of the treatments, including the controls, were carried out in duplicate.   The experiment was performed under the semistatic conditions with a complete renewal of exposure medium every three days. At the age of 4 months, part of F1 fish was sampled for gene expression analyses.

value: liver

value: 4 months old

value: female


title: C1_F1 (IM study)

description: pool of 2 individuals


title: C2_M3 (IM study)

description: pool of 2 individuals

value: IM, 1 µg/L


title: C1_M2 (IM study)

description: pool of 2 individuals


title: GAR1428

value: UCP1/FGF12 double KO


title: C1_M3 (IM study)

description: 1 individual


title: Control_M3 (IM study)

description: pool of 2 individuals


title: C1_F2 (IM study)

description: pool of 2 individuals


title: C2_M1 (IM study)

description: pool of 2 individuals


title: C2_F1 (IM study)

description: pool of 2 individuals


title: Control_M2 (IM study)

description: pool of 2 individuals


title: C2_F3 (IM study)

description: pool of 2 individuals


title: P9_E

city: Toronto

first: Paul

last: Delgado-Olguin

state: Ontario

department: Molecular Genetics

country: Canada

institute: University of Toronto

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing reads were trimmed using Trimmomatic then mapped to the mouse genome (mm10) using STAR50
Mapped read counts were obtained using featureCounts51.
Differential expression analysis was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Allsamples_DE_P1VsP9.txt file was generated using DESeq2 and contains normalized counts in addition to adjusted Pvalues and log fold change. The *.counts files are the raw counts generated from featurecounts which served as the input for Deseq2.

molecule: polyA RNA

source_name: P9_intetsinal endothelial cells

extract_protocol:
GFP positive endothelial cells were isolated from Rosa26mT/mG/+;Tie2-Cre pups by fluorescence activated cell sorting. RNA was isolated using the TRIzol® Plus RNA Purification Kit (Zymo research).
cDNA synthesis was performed with SMART-Seq Ultra low input RNA kit (Clontech laboratories). cDNA library was then prepared used the Nextera XT Library Preparation Kit (Illumina Inc).

value: Postnatal day9

value: Intestine

value: Endothelial cells


title: Control_M1 (IM study)

description: pool of 2 individuals


title: GAR1427


title: P9_B


title: C2_M2 (IM study)

description: pool of 2 individuals


title: Control_F2 (IM study)

description: pool of 2 individuals


title: C1_M1 (IM study)

description: pool of 2 individuals


title: GAR1426


title: P9_C


title: Control_F3 (IM study)

description: 1 individual


title: Control_F1 (IM study)

description: pool of 2 individuals


title: P9_D


title: P1_D

source_name: P1_intetsinal endothelial cells

value: Postnatal day1


title: GAR1423

value: UCP1 KO


title: GAR1422


title: GAR1424


title: GAR1425


title: P1_C


title: GAR1420


title: P1_B


title: C2_F2 (IM study)

description: 1 individual


title: TG2A_SMC1_M_PFA_1

value: embryonic stem cell

value: SMC1 (Bethyl Laboratories A300-055A)

value: M


title: TG2A_INPUT_M_PFA_1

value: INPUT


title: TG2A_INPUT_I_PFA_1

value: I


title: TG2A_SMC1_M_PFA_2


title: P1_A


title: GAR1419

value: inguinal white fat (iWAT)

value: WT


title: TG2A_CTCF_M_PFA_2

value: CTCF (Active Motif 61311)


title: TG2A_SMC1_I_PFA_1


title: GAR1418

value: male


title: GAR1415


title: TG2A_CTCF_I_PFA_2


title: GAR1417


title: GAR1421


title: TG2A_CTCF_I_PFA_1


title: GAR1416


title: miRNA_FF78

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Agilent miRNA hybridization protocol

scan_protocol: Standard Agilent scanning protocol

data_processing: The data were processed and normalised using the Bioconductor limma implementation in R

source_name: tumor

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Agilent MicroRNA Expression Profiling Assay Guide).

extract_protocol: RNA was extracted with  FFPE miRNeasy kit in accordance with manufacture's protocol (QIAGEN).

tag: histology

value: embrional

tag: tissue source

value: tumor


title: miRNA_FE48

value: F

value: alveolar


title: miRNA_FE58


title: miRNA_FE41

source_name: normal

value: normal


title: miRNA_FF77


title: miRNA_FE37


title: miRNA_FE34


title: FE48

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Gene-level signal were derived from CEL files using RMA algorithm implemented in oligo Bioconductor package. Batch effects were corrected using ComBat.

label: biotin

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Affymetrix).

extract_protocol: RNA was extracted with  miRNeasy FFPE kit (Qiagen) in accordance with the manufacture's protocol.


title: FF78


title: miRNA_FE61


title: FE41


title: FE61


title: miRNA_FF79


title: FF77


title: FE37


title: miRNA_FF92


title: FE58


title: P9_A

tag: strain

value: Postnatal day9

tag: tissue

value: Intestine

value: Endothelial cells


title: FF92

tag: age


title: FE34


title: FE18


title: FF79


title: FF64


title: miRNA_FF64


title: FG01


title: miRNA_FE18


title: FE39


title: miRNA_FG01


title: GAR1410

value: brown fat (BAT)

value: FGF21 KO


title: TG2A_CTCF_M_PFA_3

value: embryonic stem cell

value: M


title: miRNA_FE39


title: miRNA_FF80


title: miRNA_FF93


title: miRNA_FE11


title: miRNA_FE55


title: miRNA_FE46


title: Female_PS_5

description:
miRNA expression in microglia
miRNA_all_counts

source_name: Freshly isolated adult microglia

extract_protocol:
mirVana™ miRNA Isolation Kit, with phenol was used for RNA isolation
Total RNA (100 ng) was used for adapter ligation with the  Total RNAseq Kit v2 (Life Technologies, 4475936) and subsequently run on a 1% Tris-borate-  EDTA acrylamide gel followed by gel extraction of small RNA (45–60 bp). The small RNA  fraction was used for downstream reactions to build a small RNA library.

value: Freshly isolated adult microglia

value: 6 months

tag: Sex

value: Female


title: FF93


title: FE11


title: Female_PS_4

tag: cell type


title: miRNA_FE69


title: Female_PS_3


title: FE46


title: miRNA_FG02


title: FE55


title: FE69


title: Female_PS_2


title: FG02


title: Male_PS_5

value: Male


title: miRNA_FE49


title: FE56


title: FE16


title: Male_PS_4


title: FE49


title: FF70


title: FE17


title: miRNA_FF70


title: FF80


title: Male_PS_2


title: FF55


title: Male_PS_1


title: miRNA_FE17


title: FF62


title: miRNA_FF55


title: miRNA_FF62


title: Female_2


title: TG2A_CTCF_M_PFA_1

value: CTCF (Active Motif 61311)


title: Female_1


title: Male_4


title: miRNA_FE13


title: Male_3


title: Male_1


title: FE13


title: Male_2


title: miRNA_FE56

value: embrional


title: Female_4


title: FG00

value: tumor


title: Male_PS_3


title: FE57

value: F


title: miRNA_FG00

value: alveolar


title: miRNA_FE36


title: FF75


title: miRNA_FF75


title: miRNA_FG05


title: FG03


title: miRNA_FG03


title: miRNA_FE52


title: miRNA_FG04


title: Female_3


title: miRNA_FE57


title: miRNA_FE12


title: FF73


title: FG04


title: miRNA_FF71


title: miRNA_FF73


title: FE35


title: FF71


title: FG05


title: FF96


title: miRNA_FF96


title: miRNA_FE35


title: FE52


title: miRNA_FE15


title: FG06


title: miRNA_FG06


title: FE36


title: miRNA_FF63


title: FF63


title: miRNA_FF91


title: FE15


title: FG07


title: miRNA_FE16


title: miRNA_FE51


title: miRNA_FE54


title: RNAseq_SI_ECM_r4

city: Pozzuoli

first: Lucio

last: Di Filippo

address: Via Campi Flegrei, 34

institute: TIGEM

description: Transcriptome profile of SI_ECM_r4 sample

data_processing:
Illumina novaSeq base call (BCL) files are converted in fastq file through bcl2fastq (version v2.20.0.422)
Sequence reads were trimmed using bbduk software (bbmap suite 37.31)
Alignment was performed with STAR 2.6.0a on hg38 reference assembly obtained from cellRanger website (Ensembl 93)
The expression levels of genes were determined with htseq-count 0.9.1 by using cellRanger pre-build genes annotations (Ensembl Assembly 93)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: pediatric small intestine mucosa

growth_protocol: Small intestinal (SI) crypt stem cells and gastric crypt stem cell were isolated from pediatric small intestinal mucosa biopsies following well-established dissociation protocols (Jung et al, Nat Med 17, 1225–1227 (2011); Sato et al, Gastroenterology 141, 1762–72 (2011)). Isolated crypts were cultured in matrigel growth factor reduced (MRF) droplets.

extract_protocol:
Organoids were recovered from decellularized ECM gels and MRF control gels with 20 min incubation in Cell Recovery Solution (Corning) on ice. Cells were lysed with RLT buffer and RNA was isolated with RNeasy mini kit (Qiagen) following manufacturer instructions.
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit  (Lexogen GmbH) according to manufacturer's instructions.
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the Nova Seq 6000 (Illumina) with a read length of 100 bp
3' Digital Gene Expression

treatment_protocol: Sample Small Intestinal (SI) organoids were transferred from matrigel (MRF) culture to decellularized ECM hydrogels at 4 mg/mL concentration (30 uL droplets) and passaged weekly by manual dissociation with glass pipette. Control SI organoids were passaged in the same way from MRF to MRF.

tag: matrix

value: decellularized ECM

tag: expansion passages

tag: passages on mrf or decellularized ecm


title: FE54


title: miRNA_FF61


title: RNAseq_SI_ECM_r3

description: Transcriptome profile of SI_ECM_r3 sample


title: RNAseq_SI_ECM_r2

description: Transcriptome profile of SI_ECM_r2 sample


title: miRNA_FE50


title: RNAseq_SI_ECM_r1

description: Transcriptome profile of SI_ECM_r1 sample


title: miRNA_FG07


title: miRNA_FE20


title: FE20


title: RNAseq_SI_MRF_r4

description: Transcriptome profile of SI_MRF_r4 sample

value: matrigel growth factor reduced (MRF)


title: FF94


title: FE47


title: miRNA_FF94


title: FE50


title: RNAseq_SI_MRF_r3

description: Transcriptome profile of SI_MRF_r3 sample


title: FF61


title: RNAseq_SI_MRF_r2

description: Transcriptome profile of SI_MRF_r2 sample


title: Ccrescentus_dcdnL_rep3

city: Lausanne

first: Diego

last: Gonzalez

address: Quartier UNIL-Sorge, Bâtiment Biophore

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

hyb_protocol: Roche / NimbleGen protocol

scan_protocol: Scanning with an Agilent microarray scanner at 3 μm resolution

data_processing: Normalization with Nimblescan implemented RMA algorithm over the whole chip.

organism: Caulobacter vibrioides NA1000

source_name: Bacterial cells_dcdnL

label_protocol: Roche / NimbleGen Cy3 labelling protocol

growth_protocol: Biological triplicates of NA1000 vs NA1000-ΔcdnL grown in PYE at 28°C with agitation

extract_protocol: Trizol / Ambion RNA extraction kit

treatment_protocol: RNA extracted from 2 x 1ml OD660=0.3 for each replicate

tag: genotype/variation

value: cdnL (CCNA_00690) deletion mutant


title: Ccrescentus_dcdnL_rep2


title: Ccrescentus_dcdnL_rep1


title: miRNA_FE40


title: miRNA_FE47


title: FE21


title: RNAseq_SI_MRF_r1

description: Transcriptome profile of SI_MRF_r1 sample


title: TREATED rep3

city: Barcelona

first: Sebastián

middle: Rodrigo

last: Najle

state: Catalonia

address: Passeig Maritim de la Barceloneta, 37-49

country: Spain

institute: Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra)

data_processing:
Base calls were made using the Illumina CASAVA pipeline, with base quality encoded in phred 33
Quality of raw reads was evaluated using FastQC (v0.11.5) and MultiQC (v0.9)
Sequence reads were trimmed using Trimmomatic (v0.36) [ILLUMINACLIP:2:30:10, LEADING:25, TRAILING:25, SLIDINGWINDOW:10:30 MINLEN:50; only the non-default parameters are specified], to remove sequencing adaptors and library-specific barcode sequences and filtered with a quality score threshold < 30
Transcript abundances were estimated using kallisto in pair-end mode, with 50 bootstrap replicates
Differential gene expression analysis was performed with DESeq2 package (v1.16.1) implemented in R (v3.4.3).
Genome_build: T. thermophila reference genome (June 2014 release, available at http://ciliate.org/)
Supplementary_files_format_and_content: tab-delimited text file include TPM values for each sample.

organism: Tetrahymena thermophila

source_name: Liquid culture cells

growth_protocol: Cells were grown in 250 ml flasks containing 100 ml SPP medium of the following composition (weight/vol): 1% beef peptone, 0.1% yeast extract, 0.2% glucose and 0.003% iron citrate. The cultures were incubated in a rotatory shaker at 150 rpm and 30 °C.

extract_protocol:
For every biological replicate, 1.5 x 106 cells were collected by centrifugation at 360 ug for 2 min at 4 °C and the cell pellets were immediately resuspended in 750 ul of RNAprotect cell reagent (Qiagen), chilled on ice and conserved overnight at -20 °C. Total RNA was extracted using the RNeasy Protect Cell Mini Kit with the Qiashredder (Qiagen, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Once the cultures reached the exponential phase of growth (5 x 106 cells/ml) they were divided into two aliquots. One aliquot was induced by adding 5 ug/ml cholesterol, from a 5 mg/ml stock solution prepared in absolute ethanol. This corresponds to the “treated” experiment. The other aliquot was added an equal amount of ethanol and used as “control”.

value: cholesterol


title: miRNA_FE21


title: Ccrescentus_wt_rep2

source_name: Bacterial cells_WT

value: wild-type


title: Ccrescentus_wt_rep1


title: Vas3

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

institute: University of Zurich

data_processing:
Basecalls performed using illumina's bcl2fastq 2.19.0
Sequenced reads were trimmed for adaptor sequence, low complexity and low quality sequences. Then reads were aligned to Ensembl GRCh38.p10 genome assembly using STAR 2.6.1c with following parameters: '--outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif'
Counts were generated by Rsubread 1.32.1 with the following parameters: 'Multimapping reads : primary only', 'Multi-overlapping reads : counted', 'Overlapping bases : 10'

source_name: skin

growth_protocol: Skin from patients were transplanted on the back of an immunocomprimised mice, and treated with different topical therapies. On day 35 post-transplantation, human skin was harvested for RNA extraction

extract_protocol:
RNA was extracted with Fibrous Tissue Kit from QIAGEN
Library was prepared with SMARTer Stranded Total RNA-Seq Kit - Pico Mammalian Kit (Clonetech) and sequenced on a NovaSeq S1 Flowcell in single end 101bp mode.

tag: condition

value: Vaseline

tag: subject


title: miRNA_FF72


title: FE40


title: FF72


title: TREATED rep2

tag: treatment


title: Vas2


title: Female_PS_1


title: FE10


title: FF76


title: FE14

value: normal


title: miRNA_FE14

value: M


title: TREATED rep1


title: FE51


title: CONTROL rep3

value: control


title: NLE3

value: Non-lesion


title: Vas1


title: miRNA_FF76


title: CONTROL rep2


title: miRNA_FE10


title: NLE2


title: CONTROL rep1


title: NLE1


title: MG3

value: MTX-GNP


title: Pol5-HTP

city: Goettingen

first: Markus

middle: T.

last: Bohnsack

address: Humboldtallee 23

department: Institute for Molecular Biology

institute: Goettingen University

data_processing:
Sequencing reads for each experimental sample were demultiplexed using their 5' barcode sequences and barcodes were then clipped
Reads of identical sequence that contained identical 5-nucleotide random barcodes were collapsed
Reads were trimmed and quality controlled using flexbar and aligned to the S.cerevisiae genome by Bowtie2 (version 2.3.4.2).
Genome_build: EF2.59.1.0
Supplementary_files_format_and_content: tab-delimited text files showing the numbers of reads mapping to different classes of RNA (overviews) and the number of reads mapping to each nucleotide of the RDN37 clouc encoding the 35S pre-rRNA (35S)

organism: Saccharomyces cerevisiae

source_name: BY4741 yeast strain

growth_protocol: Wild-type BY4741 yeast cells or yeast cells expressing C-terminally His-Tev-ProtA tagged Pol5 from their genomic loci were grown in exponential phase.

extract_protocol:
Crosslinked RNA-protein complexes were purified under denaturing conditions and RNAs associated with His-ProtA-tagged proteins were trimmed (Bohnsack et al., 2012).
3' and 5' adapters were ligated and a cDNA library was prepared by reverse transcription and amplified by PCR (Bohnsack et al., 2012).

treatment_protocol: Cells were crosslinked in culturo using light at 254 nm

tag: strain background

value: expressing genomically C-terminally His-Tev-ProtA-tagged Pol5


title: miRNA_FE59


title: FF69


title: FE71


title: WT-HTP

value: wild type


title: miRNA_FF69


title: MINCE_EdU_Chase_1

source_name: embryonic stem cell

value: embryonic stem cell

tag: cell subtype

tag: cell cycle

value: R


title: LE3

value: Lesion


title: FF74

tag: gender

tag: histology

value: embrional

value: tumor


title: P654_20% oxygen cultured

city: Vancouver

first: Alexander

middle: G

last: Beristain

state: BC

address: 950 West 28th Ave

department: Obstetrics & Gynecology

institute: The University of British Columbia

description: Gene expression from matrigel embedded extravillous and column cells

hyb_protocol: Standard affymetrix hybridization protocol

scan_protocol: Standard affymetrix scanning protocol

data_processing: The Oligo package for Bioconductor was used to read raw array data into the RStudio software and convert Affymetrix CEL files into an expression matrix of intensity values. Data pre-processing included background corrrection and normalization through a Robust Multichip Average (RMA) methodology in the Oligo package. This strategy allows for background subtraction, quantile normalization and summarization via median-polish. We also conducted soft intensity-based probe filtering using the Limma package. A total of 8,352 low intensity probes, 732 duplicate probes and 4,703 non-annotated probes were filtered out to generate the final clean dataset of 13,402 probes total.

source_name: 5.2 week human placental explant cultured in 20% oxygen

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix GeneChip Whole Transcript (WT) Expression Arrays Protocol

growth_protocol: 5-8 week placental villi were microdisected from whole placenta and embedded in Matrigel matrix. Explants were cultured in DMEM F12 1:1 + penicillin-streptomycin + antibiotic-antimycotic

extract_protocol: RNA was isolated from extravillous and column cells using a protocol that combines Trixol LS + Qiagen clean-up columns + DNAse treatment to remove any contaminant gDNA. Quality control was performed using Agilent Bioanalyzer.

treatment_protocol: All explants were established in 5% oxygen for 24 hours and then subjected to another 48 hours of culture in either 1%, 5% or 20% oxygen.

value: Placental explant

value: 20% oxygen


title: FE59

tag: tissue source


title: RNA-Seq Data from green fruit skin 4

city: Hangzhou

first: Yuezhi

last: Wang

state: Zhejiang

address: Shiqiao Road No.139

institute: Zhejiang Academy of Agricultral Sciences

data_processing:
The data quality control was performed by removing adapters and discarding poor quality reads from the raw data.
Alignment of the selected reads with the reference genome of Chinese white pear (Pyrus × bretschneideri) deposited in NCBI database was carried out by Hisat2 v2.0.4
Transcripts were assembled and annotated from the read alignment results by Cufflinks v2.1.1 with the method based on the reference annotation.
The gene expression levels was quantified by FPKM method. The DESeq R package (1.18.0) was employed for gene differential expression analysis.
Benjamini and Hochberg’s approach False Discovery Rate was used for multiple test correction.
Genome_build: Chinese white pear genome as the reference
Supplementary_files_format_and_content: tab delimilted file

organism: Pyrus pyrifolia

source_name: fruit skin

growth_protocol: Open growth condition

extract_protocol:
in liquid nitrogen
NEB Next® Ultra™ RNA Library Prep Kit (NEB, USA)

treatment_protocol: Healthy plant

tag: cultivar

value: Suisho

tag: time

value: 80 DAA

tag: phenotype

value: green

tag: tissue

value: fruit skin


title: RNA-Seq Data from green fruit skin 3


title: LE2


title: MINCE_EdU_Pulse_1

tag: cell type


title: MINCE_Input_Chase_1


title: P654_1% oxygen cultured

source_name: 5.2 week human placental explant cultured in 1% oxygen

value: 1% oxygen


title: RNA-Seq Data from green fruit skin 2


title: LE1


title: P647_20% oxygen cultured

source_name: 7.1 week human placental explant cultured in 20% oxygen


title: P647_5% oxygen cultured

source_name: 7.1 week human placental explant cultured in 5% oxygen

value: 5% oxygen


title: MG2


title: miRNA_FF74

value: M

tag: age


title: miRNA_FE71


title: Daiv2

value: TCB


title: P654_5% oxygen cultured

source_name: 5.2 week human placental explant cultured in 5% oxygen


title: MINCE_Input_Pulse_1


title: P647_1% oxygen cultured

source_name: 7.1 week human placental explant cultured in 1% oxygen


title: Daiv1